Table 3.

DrGaP pathways analysis

MSigDB category	Gene set name	Somatic variant caller	Gene	P-value	RAREVATOR P-value
BP	SYSTEM PROCESS	VarScan	CLCN1	0.0054	0.0051
CM	MODULE 46	VarScan	CR1	0.0009	0.0009
CM	MODULE 75	VarScan	CR1	0.0032	0.0031
REACTOME	IMMUNE SYSTEM	muTect	CR1	0.0103	0.0099

Significantly mutated pathways identified by DrGaP algorithm by using the somatic mutations detected by MuTect and VarScan2 on the uveal melanoma dataset. The table reports the p-value calculated by DrGaP on MuTect and VarScan2 mutations, with and without the RRA variants. Columns report the MSigDB gene set category, the gene set name, the algorithm used for calling somatic variants, the RRA gene that belong to gene set, the DrGaP p-values calculated on the somatic variants (p-value) before and after the addition of the RRA variants detected by RAREVATOR (RAREVATOR P-value).